Last week, my colleagues and I did something defense attorneys rarely do: We asked the government to file charges against our client. And because it seems unlikely the case will ever make it to an American courtroom, we have asked that it be heard in the nation’s flawed military commission system.

Abu Zubaydah, our client, was an early poster child for the Bush administration’s torture regime. He was the first prisoner held in a secret “black site” and the first to be tortured using “enhanced interrogation” techniques. The infamous torture memo of August 2002 was written to clear away legal barriers that stood between him and CIA contractor interrogators. As far as we know, he is the only prisoner whose interrogation was the subject of high-level discussion in the White House and the only prisoner subjected to every enhanced technique the U.S. had authorized.

When Abu Zubaydah was arrested in March 2002, American officials vilified him. The Justice Department lawyers who wrote the torture memo described him as Osama bin Laden’s “senior lieutenant.” They said he was involved “in every major terrorist plot” carried out by al-Qaeda and that he was one of the planners of the Sept. 11 attacks. President Bush said he was a “trusted associate” of Osama bin Laden and vowed that he would be prosecuted.

After his initial interrogation by the FBI didn’t produce anything remotely like what they had expected, government officials seemed certain he was hiding something. That’s why they decided to torture him.

First, they beat Abu Zubaydah, as authorized by the torture memo. Interrogators wrapped a towel around his neck and smashed him repeatedly into a wall. He was left confined in a tiny, pitch-dark box for hours; he was suspended naked from hooks in the ceiling; he was not allowed to sleep for days on end.

He was also subjected to waterboarding, 83 times in August 2002 alone. In fact, the CIA brass at Langley ordered his interrogators to keep at it long after agents on the scene warned that he had been wrung dry.

One can question whether that kind of interrogation is ever justifiable, but in Abu Zubaydah’s case it was particularly disturbing because the outlandish allegations against him were wrong. The United States no longer believes he was even a member of al-Qaeda, let alone a trusted associate or senior lieutenant of bin Laden.

Journalist Ron Suskind was the first to question those depictions. In his 2006 book, “The One Percent Doctrine: Deep Inside America’s Pursuit of Its Enemies Since 9/11,” he concluded that Abu Zubaydah had been a minor logistics man, in essence a travel agent.

In 2009, both The Washington Post and The New York Times ran stories raising questions about the Bush administration’s portrayal of Abu Zubaydah. The Post quoted a Justice Department official who described him as having provided militants with “above-ground support” and concluded that “to make him the mastermind of anything is ridiculous.” The Times, relying on current and former intelligence officers, called the initial assessment “highly inflated” and said it reflected “a profound misunderstanding” of Abu Zubaydah’s role, which was as a sort of “personnel clerk.”

Contrary to what Bush promised, Abu Zubaydah has never been charged in the military commission system. It would be far simpler for the United States to forget about him, to just keep him locked up and hope people would one day forget. And that’s why we have asked that charges be brought.

No one should misunderstand what we have done. We don’t believe the military commission system is fair. In fact, we think its proceedings bear only a glancing resemblance to a real trial. But Abu Zubaydah has been in custody for more than 10 years without being able to answer his accusers, or even know what he is accused of. We’ve come to the conclusion that a prosecution in a flawed system is better than nothing.

At least in the commission system the government would have to put up or shut up. And it’s about time that happened.

Joseph Margulies, assistant director of the Roderick MacArthur Justice Center at Northwestern University School of Law, is counsel for Abu Zubaydah.

There is no rhyme or reason, and nothing that could pass for a justifiable goal or an ounce of sense, in the infliction of misery on the 800,000 federal employees either on furlough or working without pay.